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Open Life Sciences

formerly Central European Journal of Biology

Editor-in-Chief: Ratajczak, Mariusz

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Volume 9, Issue 12


Volume 10 (2015)

Methylation-specific PCR: four steps in primer design

Radoslav Davidović / Ana Božović / Vesna Mandušić / Milena Krajnović
Published Online: 2014-08-17 | DOI: https://doi.org/10.2478/s11535-014-0324-z


Methylation-specific PCR (MSP) is still the method of choice for a single gene methylation study. The proper design of the primer pairs is a prerequisite for obtaining reliable PCR results. Despite numerous protocols describing the rules for MSP primer design, none of them provide a comprehensive approach to the problem. Our aim was to depict a workflow for the primer design that is concise and easy to follow. In order to achieve this goal, adequate tools for promoter sequence retrieval, MSP primer design and subsequent in silico analysis are presented and discussed. Furthermore, a few instructive examples regarding a good versus a poor primer design are provided. Finally, primer design is demonstrated according to the proposed workflow. This article aims to provide researchers, interested in a single gene methylation studies, with useful information regarding successful primer design.

Keywords: Methylation-specific PCR; Primer Design; Database; Software for MSP Primer Design; Transcriptional Start Site

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About the article

Published Online: 2014-08-17

Published in Print: 2014-12-01

Citation Information: Open Life Sciences, Volume 9, Issue 12, Pages 1127–1139, ISSN (Online) 2391-5412, DOI: https://doi.org/10.2478/s11535-014-0324-z.

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